Protein Structure Prediction and Analysis Tools

Question 1

Database used for structure visualization?

Answer 1

Rasmol
MDL Chime
Protein explorer
Jmol
Pymol

Question 2

Database for structure analysis?

Answer 2

DSSP server

Question 3

What is DSSP CODE?

Answer 3

H = alpha helix
G = 3-helix (3/10 helix)
I = 5 helix (pi helix)
B = residue in isolated beta-bridge
E = extended strand participates in beta ladder
T = hydrogen bonded turn
S = bend
Blank = loop

Question 4

What is Solvent Accessibility?

Answer 4

Size of the area of an amino acid that is exposed to solvent (water). Maximum solvent accessible area for each amino acid is its whole surface area.

Question 5

Structure Alignment Tools

Answer 5

Dali
TM align
CE

Question 6

1D Structure Prediction

Answer 6

Secondary structure
Solvent accessibility
Disordered regions
Domain boundary

Question 7

tools used for 1D Structure Prediction?

Answer 7

SSpro 4.1:
Distill:
PSI-PRED:
SAM
PHD

Question 8

Tools used for Solvent Accessibility Prediction?

Answer 8

ACCpro 4:1
SCRATCH
PHD
Distill

Question 9

Tools used for Disordered Region Prediction Using Neural Networks

Answer 9

PreDisorder
PrDos
DISOPRED3
POODLE

Question 10

Contact Map Prediction

Answer 10

A protein contact map represents the distance between all possible amino acid residue pairs of a
three-dimensional protein structure using a binary two-dimensional matrix.

Question 11

Tools used in contact prediction?

Answer 11

SVMcon
NNcon
SCRATCH
SAM

Question 12

Template-Based Structure Prediction

Answer 12

Template identification
Query-template alignment
Model generation
Model evaluation
Model refinement
if the template is easy to identify, it is often called comparative Modeling or homology modeling. If the template is hard to identify, it is often called fold recognition.

Question 13

3D Structure Prediction Tools

Answer 13

MULTICOM
I-TASSER
ROBETTA
3D-JURY
FFAS
Pcons
sparks
sam
3d-pssm